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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:51:01 +0000
parents
children 42f3a9cab210
files qiime2__feature_classifier__fit_classifier_naive_bayes.xml test-data/.gitkeep
diffstat 1 files changed, 151 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__feature_classifier__fit_classifier_naive_bayes.xml	Mon Aug 29 19:51:01 2022 +0000
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+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2022, QIIME 2 development team.
+
+Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
+-->
+<!--
+This tool was automatically generated by:
+    q2galaxy (version: 2022.8.1)
+for:
+    qiime2 (version: 2022.8.1)
+-->
+<tool name="qiime2 feature-classifier fit-classifier-naive-bayes" id="qiime2__feature_classifier__fit_classifier_naive_bayes" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Train the naive_bayes classifier</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version feature_classifier</version_command>
+    <command detect_errors="aggressive">q2galaxy run feature_classifier fit_classifier_naive_bayes '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="reference_reads" type="data" format="qza" label="reference_reads: FeatureData[Sequence]" help="[required]">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Sequence]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
+        </param>
+        <param name="reference_taxonomy" type="data" format="qza" label="reference_taxonomy: FeatureData[Taxonomy]" help="[required]">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Taxonomy]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="class_weight" type="data" format="qza" optional="true" label="class_weight: FeatureTable[RelativeFrequency]" help="[optional]">
+                <options options_filter_attribute="metadata.semantic_type">
+                    <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+                </options>
+                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator>
+            </param>
+            <param name="classify__alpha" type="float" value="0.001" label="classify__alpha: Float" help="[default: 0.001]"/>
+            <param name="classify__chunk_size" type="integer" value="20000" label="classify__chunk_size: Int" help="[default: 20000]"/>
+            <param name="classify__class_prior" type="text" value="null" label="classify__class_prior: Str" help="[default: 'null']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="classify__fit_prior" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="classify__fit_prior: Bool" help="[default: No]"/>
+            <param name="feat_ext__alternate_sign" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="feat_ext__alternate_sign: Bool" help="[default: No]"/>
+            <param name="feat_ext__analyzer" type="text" value="char_wb" label="feat_ext__analyzer: Str" help="[default: 'char_wb']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feat_ext__binary" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="feat_ext__binary: Bool" help="[default: No]"/>
+            <param name="feat_ext__decode_error" type="text" value="strict" label="feat_ext__decode_error: Str" help="[default: 'strict']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feat_ext__encoding" type="text" value="utf-8" label="feat_ext__encoding: Str" help="[default: 'utf-8']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feat_ext__input" type="text" value="content" label="feat_ext__input: Str" help="[default: 'content']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feat_ext__lowercase" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="feat_ext__lowercase: Bool" help="[default: Yes]"/>
+            <param name="feat_ext__n_features" type="integer" value="8192" label="feat_ext__n_features: Int" help="[default: 8192]"/>
+            <param name="feat_ext__ngram_range" type="text" value="[7, 7]" label="feat_ext__ngram_range: Str" help="[default: '[7, 7]']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feat_ext__norm" type="text" value="l2" label="feat_ext__norm: Str" help="[default: 'l2']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feat_ext__preprocessor" type="text" value="null" label="feat_ext__preprocessor: Str" help="[default: 'null']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feat_ext__stop_words" type="text" value="null" label="feat_ext__stop_words: Str" help="[default: 'null']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feat_ext__strip_accents" type="text" value="null" label="feat_ext__strip_accents: Str" help="[default: 'null']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feat_ext__token_pattern" type="text" value="(?u)\b\w\w+\b" label="feat_ext__token_pattern: Str" help="[default: '(?u)\\b\\w\\w+\\b']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feat_ext__tokenizer" type="text" value="null" label="feat_ext__tokenizer: Str" help="[default: 'null']">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="verbose" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="verbose: Bool" help="[default: No]"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="classifier" format="qza" label="${tool.name} on ${on_string}: classifier.qza" from_work_dir="classifier.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: feature-classifier fit-classifier-naive-bayes
+======================================================
+Train the naive_bayes classifier
+
+
+Outputs:
+--------
+:classifier.qza: &lt;no description&gt;
+
+|  
+
+Description:
+------------
+Create a scikit-learn naive_bayes classifier for reads
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="bibtex">@article{cite1,
+ author = {Pedregosa, Fabian and Varoquaux, Gaël and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, Édouard},
+ journal = {Journal of machine learning research},
+ number = {Oct},
+ pages = {2825--2830},
+ title = {Scikit-learn: Machine learning in Python},
+ volume = {12},
+ year = {2011}
+}
+</citation>
+        <citation type="doi">10.1186/s40168-018-0470-z</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>